I'm looking for resources that best describe picking and using colors within a user interface. For example, elements that are good to color and elements that should have no or little color impact. I have a user interface that may be subject to many themes depending on its usage. Theming will mostly be limited to color, logos and similar content. We would like to keep the experience similar for themes and therefore are unlikely to change element appearances (corners, whether or not accents are present, animations and other behaviors).

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I answered a similar question on choosing a color scheme. In addition to that answer, to answer your question about what should have color impact, you should give special emphasis to elements that matter to the user and what they're trying to accomplish. Keep in mind, however, that color shouldn't be the sole way that this is indicated. Accessibility for color blind users is important and so size, text, whitespace, and shape all play a role as well.